Evidence for the Evolutionary Model

Primer Designer

This page/program is a modification of the Dana-Farber Cancer Institute's 'Oligo Calculator'


Ciona intestinalis genome: Ghost Database




UTR Remover

Enter Gene Sequence in Box
Enter Translated Sequence in Box
Gene Sequence without UTRs

Gene is Reverse Complimented




Intron/Exon Constructer

Enter Results From CLUSTAL 2.1 multiple sequence alignment in Box
Constructed Gene
Amplicon Length:       Percent Deviation:%       Percent Intron:%





Oligo Finder

Enter Exon/Intron Sequence in Box
Reading Frame:
Melting Temp (deg C): Min: Max:
%GC Content: Min: Max:
Primer Length: Min: Max:
Amplicon Length: +/-
Maximum Intron Proportion: %
Primer Root Name: Primer 1 Designation:
Primer 2 Designation:
Find Pair with: lowest intron base count
lowest intron proportion
lowest amplicon deviation
Matching Primers: Matching Pairs:
Best Matching Pair





Primer Alignment

Enter Genome Sequence in Box
Extract Gene Sequence from:
Genome Name:       Gene Name:
Reverse Complimented:       Genome     Gene
Include Genome FASTA:  
Alignment FASTA